Preheat the oven to 350 degrees Fahrenheit.
Whisk together all wet ingredients.
Add in the dry ingredients aside from the chocolate chunks and combine with a wooden spoon.
Fold in the chocolate chunks until evenly incorporated. Let sit in the fridge for just about 5-10 minutes to allow the flours to absorb some extra moisture. Coconut flour is very absorbent, so the dough doesn't need to chill for long.
Use a spoon or cookie scoop and scoop the dough into about 1 1/2 to 2 inch balls. Press extra chocolate chunks or chips on top.
Bake for 9-13 minutes (I usually do 10 for soft cookies or 11 if I want the edges slightly crunchier but still keep soft centers) and then let cool.
The cookies will continue to harden as they cool, so if you want them to stay chewy, take them out of the oven when they still look slightly raw in the middle but have slightly golden brown edges. If you like slightly crunchier cookies, just bake for closer to 13 minutes!
Use a round cookie cutter to carefully scoot the cookies into a perfectly round shape as soon as they come out of the oven. Sprinkle with salt flakes and enjoy!